If we decide to move to single sign-on in Windows Intune, do we need to uninstall / reinstall the Intune agents on our desktops?
Is there good documentation of what steps we must take if we move from onmicrosoft.com accounts to organizational accounts or ADFS?
No, you wouldn't need to reinstall the agents. The clients use certificate based authentication to communicate to the service, not a username and password.
As long as you use the same tenant account, no reinstall would be needed.
Here is a guide on setting up ADFS:
Jon L. - MSFT - This posting is provided "AS IS" with no warranties and confers no rights.
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